Today I just imported my wallet to blockchain.info and inmediatly notice there is 3.6 bitcoins missing!

Aparently its just one transaction that is missing in blockchain.info, taking a look at the wallet in bitcoin-qt in my computer I just notice this transaction was recieved using a address that dont appear anymore in my list of incoming addresses. Is there something I can do to resolve this issue? I'm a bit worried that this transaction could be lost...

if you don't have access to that address at all I don't think there is much you can do. I have been experimenting with pywallet, bitcoin-qt, and electrum.. using pywallet you can get an to an addresses private key, and then import that address into electrum (along with any funds attached). I don't know if you can do something similar with blockchain.info or not. Sorry for the rant, I'm just not sure if you have access to the address in question or not.. so I kind of rambled.

I'm taking a look at electrum, looks pretty nice, I will try it later.

I was thinking maybe I will try to make a new wallet and transfer all my bitcoins there, just to make sure there wont be trouble with that missing address and blockchain.info. I just hope nothing got corrupted or loose some bitcoins

You said you imported your wallet into blockchain.info, but you didn't say where it came from. If it came from the Bitcoin-QT client, then can you start up your Bitcoin-QT wallet and see if it still shows those 3.6 bitcoins there? If so, then the bitcoins are probably still recoverable. If not, then the odds are a lot worse.

Yes I'm using bitcoin-qt, and the transaction still show there in my transaction history and the total amount of bitcoins remains correct, its just the address that dont appear in the address list to receive bitcoins and I think thats what causing trouble with the import to blockchain.info. I think the best solution is to transfer all bitcoins to a new wallet just in case to avoid any trouble with that transaction, I will try it later today and see how it goes (cross fingers ^^).

The 3.6 BTC was sent to a hidden "change" address. You REALLY (and by REALLY I MEAN REALLY REALLY REALLY REALLY) shouldn't be swaping keys between multiple clients/wallets. It is a very good way to end up with very bizarre behavior.

You can either dump all private keys in your wallet and import all of them to blockchain.info or you can send all your coins to a address you do know.

As D&T points out, those bitcoins are likely associated with a "change" address. If you have ever sent any bitcoins from your Bitcoin-Qt wallet to anywhere else, then your Bitcoin-Qt wallet creates a hidden address where it stores the change from the transaction.

With the way bitcoin works, you can't partially spend a previous output that you received. It has to be completely spent. So, if you receive 10 BTC all in a single transaction from someone/somewhere at an address (lets use 1MyBitcoinAddress as an example), then that address now has a single 10 BTC output.

Later if you want to send 4 BTC to somebody, the program can use the previous 10 BTC output as an input into the transaction, and create a 4 BTC output to the address where you want to send it. This leaves 6 BTC leftover in the transaction. If you don't send those 6 BTC somewhere, then they become miner fees and end up in the coinbase transaction of the new block for the miner to keep. If you don't want to give those 6 BTC away as fees to the miner, then you need to include a second output in your transaction sending the 6 BTC back to your own wallet. As an analogy, think of pulling a $10 bill out of your pocket to pay for something that costs $4, you get $6 back in "change".

The way Bitcoin-Qt does this is to create a new bitcoin address that it doesn't tell you about and keep track of that address and the associated private key in your wallet.dat. Since this isn't an address that you requested in the "Receive Coins" tab of the user interface, it doesn't show up in that list. Bitcoin-Qt knows about the address since it is in the wallet.dat file, so it includes it in the balance that it shows you. Bitcoin-Qt uses a new change address for every transaction. So if you create 10 different transactions, each sending bitcoins somewhere, then your wallet will have used 10 different change addresses (although some of them may be empty if Bitcoin-Qt used the bitcoins associated with some of those address as inputs into other transactions.

As D&T said. Do not try and use 2 wallet programs with the same addresses in both. This will lead to confusion, odd wallet behavior, and eventually a complete mess. If you are trying to switch to using blockchain.info, then once you have all your bitcoins there, you need to stop using the Bitcoin-Qt wallet that has the same addresses. Since you should be using a new address for every transaction, there aren't many good reasons for importing addresses from one wallet into another. Generally it is faster, safer, and easier to just send the bitcoins from one wallet to the other.